Adamowicz, et al., "Nutritional complementation of oxidative glucose metabolism in Escherichia coli via pyrroloquinoline quinone-dependent glucose dehydrogenase and the Entner-Doudoroff pathway," Appl Environ Microbiol, 57(7):2012-2015 (1991).
|
Akutsu, "Estimation Algorithm of Genetic Network," Mathmatical Science (Suri-Kagaku) 37(6)40-46 (1999). (Original and English translation submitted herewith), Mathematical Science.
|
Alberty, "Calculation of Biochemical Net Reactions and Pathways by Using Matrix Operations," Biophys J, 71(1):507-515 (1996).
|
Alm, et al., "Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori," Nature, 397(6715):176-80 (1999).
|
Alon, et al., "Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays," Proc Natl Acad Sci U.S.A., 96(12):6745-6750 (1999).
|
Alter, et al., "Singular value decomposition for genome-wide expression data processing and modeling," Proc Natl Acad Sci U.S.A., 97(18):10101-10106 (2000).
|
Altschul, et al., "Gapped BLAST and PSI-BLAST: A New Generation of Protein Database Search Programs," Nucl Acids Res, 25(17):3389-3402 (1997).
|
Alves, et al., "Systemic properties of ensembles of metabolic networks: application of graphical and statistical methods to simple unbranched pathways," Bioinformatics, 16(6):534-547 (2000).
|
Andre, "An overview of membrane transport proteins in Saccharomyces cerevisiae," Yeast, 11(16):1575-1611 (1995).
|
Anonymous, "The yeast genome directory" Nature, 387(6632 Suppl):5 (1997).
|
Appel, et al., "A new generation of information retrieval tools for biologists: the example of the ExPASy WWW server," Trends Biochem Sci, 19(6):258-260 (1994).
|
Arigoni, et al., A Genome-Based Approach for the Identification of Essential Bacterial Genes: Nature Biotechnology, US. Nature Publishing: vol. 16:9 (1998).
|
Aristidou and Penttila, "Metabolic engineering applications to renewable resource utilization," Curr. Opin. Biotechnol. 11(2)187-198 (2000).
|
Attanoos, et al., "Ileostomy polyps, adenomas, and adenocarcinomas," Gut, 37(6):840-844 (1995).
|
Baba, et al., "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection," Mol Syst Biol, 2:2006-2008 (2006).
|
Bailey, "Complex Biology With No Parameters," Nat Biotechnol, 19(6):503-504 (2001).
|
Bailey, TL and Elkan, C, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers," Proc Int Conf Intell Syst Mol Biol, 2:28-36 (1994).
|
Bailey, TL and Gribskov, M, "Combining evidence using p-values: application to sequence homology searches," Bioinformatics, 14(1):48-54 (1998).
|
Bairoch, A, and Apweiler, R, "The SWISS-PROT Protein Sequence database and its supplement TrEMBL in 2000," Nucleic Acids Res, 28(1):45-48 (2000).
|
Ball, et al., "Integrating functional genomic information into the Saccharomyces genome database," Nucleic Acids Res, 28(1):77-80 (2000).
|
Baltz, et al., DNA Sequence Sampling of the Streptococcus pneumonia genome to identify novel targets for antibiotic development: Microbial Drug Resistant US. Liebert vol. 4, No. 1:1-9 (1998).
|
Ban, et al., "Thymine and uracil catabolism in Escherichia coli," J Gen Microbiol, 73(2):267-272 (1972).
|
Bansal, "Integrating co-regulated gene-groups and pair-wise genome comparisons to automate reconstruction of microbial pathways," Bioinformatics and Bioengineering Conference, 209-216 (2001).
|
Bard, et al., "Sterol mutants of Saccharomyces cerevisiae: chromatographic analyses," Lipids, 12(8):645-654 (1977).
|
Baxevanis, "The Molecular Biology Database Collection: 2002 update," Nucleic Acids Res, 30:1-12 (2002).
|
Beard, et al., "Energy Balance for Analysis of Complex Metabolic Networks," Biophys J, 83(1):79-86 (2002).
|
Beckers, et al., "Large-Scale Mutational Analysis for the Annotation of the Mouse Genome," Curr Opin Chem Biol, 6(1)17-23 (2002).
|
Bell, et al., "Composition and functional analysis of the Saccharomyces cerevisiae trehalose synthase complex," J Biol Chem., 273(50):33311-33319 (1998).
|
Benjamini and Hochberg, "Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing," J.R. Statist. Soc. B. 57:289-300 (1995).
|
Benson, et al., "GenBank," Nucleic Acids Res, 28(1):15-18 (2000).
|
Berry, "Improving production of aromatic compounds in Escherichia coli by metabolic engineering," Trends Biotechnol, 14(7):250-256 (1996).
|
Bialy, "Living on the Edges," Nat Biotechnol, 19(2):111-112 (2001).
|
Bianchi, P, and Zanella, A, "Hematologically Important Mutations: Red Cell Pyruvate Kinase (Third Update)," Blood Cells, Molecules, and Diseases, 15:47-53 (2000).
|
Biaudet, et al., "Micado-a network-oriented database for microbial genomes," Comput Appl Biosci, 13(4):431-438 (1997).
|
Birkholz, "Fumarate reductase of Helicobacter pylori-an immunogenic protein," J Med Microbiol, 41(1):56-62 (1994).
|
Birner, et al., "Roles of phosphatidylethanolamine and of its several biosynthetic pathways in Saccharomyces cerevisiae," Mol Biol Cell, 12(4):997-1007 (2001).
|
Blackstock, WP and Weir, MP, "Proteomics: quantitative and physical mapping of cellular proteins," Trends Biotechnol, 17(3):121-127 (1999).
|
Blattner, Frederick, The Complete Genome Sequence of Escherichia coli K-12. Science. vol. 2777, pp. 1453-1462, Sep. 1997.
|
Bochner, "New technologies to assess genotype-phenotype relationships," Nat Rev Genet, 4(4):309-314 (2003).
|
Boles, E, et al., "Identification and characterization of MAE 1 ,the Saccharomyces cerevisiae structural gene encoding mitochondrial malic enzyme," J Bacteriol., 180(11):2875-2882 (1998).
|
Boles, et al., "A family of hexosephosphate mutases in Saccharomyces cerevisia," Eur J Biochem, 220(1):83-96 (1994).
|
Boles, et al., "Characterization of a glucose-repressed pyruvate kinase (Pyk2p) in Saccharomyces cerevisiae that is catalytically insensitive to fructose-1,6-bisphosphate," J Bacteriol, 179(9):2987-2993 (1997).
|
Bonarius, et al., "Metabolic flux analysis of hybridoma cells in different culture media using mass balances," Biotechnol Bioeng, 50(3):299-318 (1996).
|
Bonarius, Hendrik, Flux Analysis of Underdetermined metabolic networks: the quest for the missing constraints. Tibtech, vol. 15, pp. 308-324, Aug. 1997.
|
Bono, et al., "Reconstruction of amino acid biosynthesis pathways from the complete genome sequence," Genome Research, 8(3):203-210 (1998).
|
Bottomley, et al., "Cloning, sequencing, expression, purification and preliminary characterization of a type II dehydroquinase from Helicobacter pylori," Biochem. J, 319(Pt 2):559-565 (1996).
|
Bourot, S and Karst, F, "Isolation and characterization of the Saccharomyces cerevisiae SUT1 gene involved in sterol uptake," Gene, 165(1):97-102 (1995).
|
Burgard, AP and Maranas, CD, "Probing the Performance Limits of the Escherichia coli Metabolic Network Subject to Gene Additions or Deletions, Biotechnol Bioeng," 74(5):364-375 (2001).
|
Burgard, AP and Maranas, CD, "Review of the Enzymes and Metabolic Pathways (EMP) Database," Metab Eng, 3(3):193-194(2) (2001).
|
Burgard, et al., "Minimal reaction sets for Escherichia coli metabolism under different growth requirements and uptake environments," Biotechnol Prog, 17(5):791-797 (2001).
|
Burgard, et al., "Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization," Biotechnol Bioeng, 84(6):647-657 (2003).
|
Burns, "Acetyl-CoA carboxylase activity in Helicobacter pylori and the requirement of increased CO2 for growth," Microbiology, 141(Pt 12):3113-3118 (1995).
|
Callis, "Regulation of Protein Degradation," Plant Cell 7:845-857 (1995).
|
Chadha et al., "Hybrid process for ethanol production from rice straw," Acta. Microbiol. Immunol. Hung. 42(1):53-59 (1995).
|
Chadha et al., "Simultaneous saccharification and fermentation of rice straw into ethanol," Acta. Microbiol. Immunol. Hung. 42(1):71-75 (1995).
|
Chalker, et al., "Systematic identification of selective essential genes in Helicobacter pylori by genome prioritization and allelic replacement mutagenesis," J Bacteriol, 183(4):1259-1268 (2001).
|
Chen, et al., "Characterization of the respiratory chain of Helicobacter pylori," FEMS Immunol Med Microbiol, 24(2):169-174 (1999).
|
Cherry, et al., "SGD: Saccharomyces Genome Database," Nucleic Acids Res, 26(1):73-79 (1998).
|
Christensen and Nielsen, "Metabolic network analysis. A powerful tool in metabolic engineering," Adv. Biochem Engi Biotech.66:209-231 (2000).
|
Ciriacy, M and Breitenbach, I, "Physiological effects of seven different blocks in glycolysis in Saccharomyces cerevisiae," J Bacteriol, 139(1):152-160 (1979).
|
Clarke, "Complete set of steady states for the general stoichiometric dynamical system," J Chem Phys, 75(10):4970-4979 (1981).
|
Clarke, "Stability of Complex Reaction Networks," Adv. Chem. Physics 43:1-125 (1980).
|
Clarke, "Stoichiometric network analysis," Cell Biophys, 12:237-253 (1988).
|
Clifton, D and Fraenkel, DG, "Mutant studies of yeast phosphofructokinase.," Biochemistry, 21(8):1935-1942 (1982).
|
Clifton, et al., "Glycolysis mutants in Saccharomyces cerevisiae.," Genetics, 88(1):1-11(1978).
|
Compan, I and Touati, D, et al., "Anaerobic activation of arcA transcription in Escherichia coli: roles of Fnr and ArcA," Mol Microbiol, 11(5):955-964 (1994).
|
Costanzo, et al., "YPD, PombePD and WormPD: model organism volumes of the BioKnowledge library, an integrated resource for protein information," Nucleic Acids Res, 29(1):75-9 (2001).
|
Cotter, et al., "Aerobic regulation of cytochrome d oxidase (cydAB) opoeron expression in Escherichia coli: roles of Fnr and ArcA in repression and activation," Mol Microbiol, 25(3):605-615 (1997).
|
Cover and Blaser, "Helicobacter pylori infection, a paradigm for chronic mucosal inflammation: pathogenesis and implications for eradication and prevention," Adv. Intern. Med. 41:85-117 (1996).
|
Covert, et al., "Metabolic Modeling of Microbial Strains In Silico," Trends Biochem Sci, 26(3):179-186 (2001).
|
Covert, et al., "Regulation of Gene Expression in Flux Balance Models of Metabolism," J Theor Biol, 213(1):73-88 (2001).
|
Covert, MW and Palsson, BO, "Constraints-based models: Regulation of Gene Expression Reduces the Steady-state Solution Space," J Theor Biol, 216 (2003).
|
Covert, MW and Palsson, BO, "Transcriptional Regulation in Constraints-based Metabolic Models of Escherichia coli," J Biol Chem, 277(31):28058-28064 (2002).
|
Cupp, JR and McAlister-Henn, L, "Cloning and Characterization of the gene encoding the IDH1 subunit of NAD(+)-dependent isocitrate dehydrogenase from Saccharomyces cerevisiae," J Biol Chem, 267(23):16417-16423 (1992).
|
Dafoe et al., "In Silico Knowledge Discovery Biomedical databases," Proceedings of the SPIE Fifth Workshop on Neural Networks, San Francisco, Nov. 7-10, 1993.
|
Danchin, "Comparison Between the Escherichia coli and Bacillus subtilis Genomes Suggests That a Major Function of Polynucleotide Phosphorylase is to Synthesize CDP," DNA Research, 4(1):9-18 (1997).
|
Dandekar, et al., "Pathway Alignment: Application to the Comparative Analysis of Glycolytic Enzymes," Biochem J, 343(Pt 1):115-124 (1999).
|
Dantigny, et al., "A new control strategy for yeast production based on the L/A* approach," Appl Microbiol Biotechnol, 36:352-357 (1991).
|
Datsenko, KA and Wanner, BL, "One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products," Proc Natl Acad Sci U.S.A., 97(12):6640-6645 (2000).
|
Daum, et al., "Biochemistry, cell biology and molecular biology of lipids of Saccharomyces cerevisiae," Yeast, 14(16):1471-1510 (1998).
|
Daum, et al., "Systematic analysis of yeast strains with possible defects in lipid metabolism," Yeast, 15(7):601-614 (1999).
|
Dauner, et al., "Bacillus subtilis Metabolism and Energetics in Carbon-Limited and Excess-Carbon Chemostat Culture," J Bacteriol, 183(24):7308-7317 (2001).
|
Dauner, et al., "Metabolic Flux Analysis with a Comprehensive Isotopomer Model in Bacillus subtilis," Biotechnol Bioeng, 76(2):144-156 (2001).
|
Dauner, M and Sauer, U, "Stoichiometric Growth Model for Riboflavin-Producing Bacillus subtilis," Biotechnol Bioeng, 76(1):132-143 (2001).
|
de Jong, H., "Modeling and simulation of genetic regulatory systems: a literature review," J Comput Biol, 9(1):67-103 (2002).
|
De Reuse, et al., "The Helicobacter pylori ureC gene codes for a phosphoglucosamine mutase," J Bacteriol, 179(11):3488-3493 (1997).
|
Delgado and Liao, "Identifying Rate-Controlling Enzymes in Metabolic Pathways without Kinetic Parameters," Biotechnol Prog, 7:15-20 (1991).
|
Demain, et al., "Cellulase, clostridia, and ethanol," Microbiol Mol Biol Rev, 69(1):124-154 (2005).
|
Department of Energy, Breaking the Biological Barriers to Cellulosic Ethanol (2006).
|
DeRisi, et al.,"Exploring the Metabolic and Genetic Control of Gene Expression on a Genomic Scale," Science, 278(5338):680-686 (1997).
|
Devine, KM, "The Bacillus subtilis Genome Project: Aims and Progress," Trends Biotechnol, 13(6):210-216 (1995).
|
D'Haeseleer, et al., "Genetic network inference: from co-expression clustering to reverse engineering," Bioinformatics, 16(8):707-726 (2000).
|
Dickson, "Sphingolipid Functions in Sacchoromyces cerevisiae: Comparison to Mammals," Annu Rev Biochem, 67:27-48 (1998).
|
Dickson, et al., "Serine palmitoyltransferase," Methods Enzymol, 311:3-9 (2000).
|
DiRusso, CC and Black, PN, "Long-chain fatty acid transport in bacteria and yeast. Paradigms for defining the mechanism underlying this protein-mediated process," Mol Cell Biochem, 192(1-2):41-52 (1999).
|
Dooley et al., "An all D-amino acid opiod peptide with central analgesic activity from a combinatorial library," Science 266(5193):2019-2022 (1994).
|
Duarte et al., "Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model," Genome Res. 14(7):1298-1309 (2004).
|
Earp, et al. Ecoye Encyclopedia of Escherichia coli Genes and Metabolism: Nucleic Acids Research, vol. 25, No. 1:43-50 (1997).
|
Earp, P.D., Metabolic databases:TIBS Trends in Biochemical Science, en. Elsevier Publication. Cambridge: vol. 23, No. 3:114-115 (1998).
|
Edwards and Palsson, "The Escherichia coli MG1655 in silico Metabolic Genotype: Its Definition, Characteristics, and Capabilities," Proc. Natl. Acad. Sci. USA 97(10):5528-5533 (2000).
|
Edwards et al., "Characterizing Phenotypic Plasticity: A Phase Plane Analysis," BMES/EMBS Conference, Proceedings of the First Joint vol. 2, p. 1217 (1999).
|
Edwards et al., Genomically Based Comparative Flux Balance Analysis of Escherichia coli and Haemophilus influenzae, Abstracts of Papers, American Chemical Society, 213(1-3): BIOT 50, San Francisco, Apr. 13-17, 1997.
*
|
Edwards et al., Journal of Biological Chemistry, 274(25):17410-17416, Jun. 18, 1999.
*
|
Edwards, et al., "Characterizing the Metabolic Phenotype: A Phenotype Phase Plane Analysis," Biotech Bioeng, 77(1):27-36 (2002).
|
Edwards, et al., "In Silico Predictions of Escherichia coli metabolic capabilities are Consistent with Experimental Data," Nat Biotechnol, 19(2):125-130 (2001).
|
Edwards, Jeremy, et al. How Will Bioinformatics Influence Metabolic Engineering Biotechnology & Bioengineering, vol. 58, No. 2-3:162-69 (1998).
|
Edwards, JS and Palsson, BO, "Robustness analysis of the Escherichia coli metabolic network," Biotechnol Prog, 16(6):927-939 (2000).
|
Edwards, JS, and Palsson, BO, "Metabolic flux analysis and the in silico analysis of Escherichia colia K-12 gene deletions," BMC Bioinformatics, 1:1-10 (2000).
|
Eisen, et al., "Cluster analysis and display of genome-wide expression patterns," Proc Natl Acad Sci U.S.A., 95:14863-14868 (1998).
|
Eisenberg, et al., "Protein Function in the Post-Genomic Era," Nature, 405(6788):823-826 (2000).
|
Ermolaeva, et al., "Prediction of Operons in Microbial Genomes," Nucl Acids Research, 29(5):1216-1221 (2001).
|
Everett, et al., Pendred syndrome is caused by mutations in a putative sulphate transporter gene (PDS). Nature Genetics vol. 17, pp. 411-422 (1997).
|
Everitt, "Cluster Analysis 122," London:Heinemann (1974).
|
Feist and Palsson, "The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli," Nat. Biotech. 26(6):659-667 (2008).
|
Fell, David. Fat Synthesis in Adipose Tissue. J. Brochen, vol. 238, pp. 781-786 (1986).
|
Fiehn, "Metabolomics—the link between genotypes and phenotypes," Plant Mol Biol, 48(1-2):155-171 (2002).
|
Finel, "Does NADH play a central role in energy metabolism in Helicobacter pylori?," Trends Biochem Sci, 23(11):412-413 (1998).
|
Fiorelli, et al., "Chronic non-spherocytic Haemolytic disorders associated with glucose-6-phosphate dehydrogenase variants," Bailliere's Clinical Haematology, 13:39-55 (2000).
|
Five pages from URL: web.archive.org/web/20050731094028/http://www.chem.qmw.ac.uk/iubmb/enzyme/ Enzyme Nomenclature database maintained by G. P. Moss of Queen Mary and Westfield Colege in the United Kingdom; Date Obtained May 15, 2009.
*
|
Fleischmann, "Whole-genome random sequencing and assembly of Haemophilus influenzae Rd," Science 269(5223):496-512 (1995).
|
Flikweert, et al., "Pyruvate decarboxylase: an indispensable enzyme for growth of Saccharomyces cerevisiae on glucose.," Yeast, 12(3):247-257 (1996).
|
Forst, "Network genomics—A Novel approach for the analysis of biological systems in the post-genomic era," Molecular Biology Reports, 29(3):265-280 (2002).
|
Forster, et al., "Large-scale evaluation of in silico gene deletions in Saccharomyces cerevisiae," Omics, 7(2)193-202 (2003).
|
Fraenkel, "The accumulation of glucose 6-phosphate from glucose and its effect in an Escherichia coli mutant lacking phosphoglucose isomerase and glucose 6-phosphate dehydrogenase," J Biol Chem, 243(24):6451-6457 (1968).
|
Fraser, et al., "Microbial genome sequencing," Nature, 406:799-803 (2000).
|
Fromont-Racine, et al., "Toward a functional analysis of the yeast genome through exhaustive two-hybrid screens," Nat Genet, 16(3):277-282 (1997).
|
Fukuchi, et al., "Isolation, overexpression and disruption of a Saccharomyces cerevisiae YNK gene encoding nucleoside diphosphate kinase," Genes, 129(1):141-146 (1993).
|
Gaasterland, T. and Selkov, E., "Reconstruction of Metabolic Networks Using Incomplete Information," Proc Int Conf Intell Syst Mol Biol, 3:127-135 (1995).
|
Galperin and Brenner; Using Metabolic Pathway Databases for Functional Annotation, pp. 332-333, Trends in Genetics, vol. 14: No. 8 (Aug. 1998).
|
Gancedo, C and Delgado, MA, "Isolation and characterization of a mutant from Saccharomyces cerevisiae lacking fructose 1,6-bisphosphatase," Eur J Biochem, 139:651-655 (1984).
|
Gangloff, et al., "Molecular cloning of the yeast mitochondrial aconitase gene (ACO1) and evidence of a synergistic regulation of expression by glucose plus glutamate.," Mol Cell Biol, 10(7):3551-3561 (1990).
|
Ge, et al., "Cloning and functional characterization of Helicobacter pylori fumarate reductase operon comprising three structural genes coding for subunits C, A and B," Gene 204(1-2):227-234 (1997).
|
Glasner, et al., "ASAP, a systematic annotation package for community analysis of genomes," Nucleic Acids Res, 31(1):147-151 (2003).
|
Goffeau, A, "Four years of post-genomic life with 6000 yeast genes," FEBS Lett, 480(1):37-41 (2000).
|
Goryanin, et al., "Mathematical simulation and analysis of cellular metabolism and regulation," Bioinformatics, 15(9):749-758 (1999).
|
Goto, et al., "LIGAND database for enzymes, compounds and reactions," Nucleic Acids Res, 27(1):377-379 (1999).
|
Goto, et al., "LIGAND: chemical database for enzyme reactions," Bioinformatics, 14(7):591-599 (1998).
|
Grewal, et al., "Computer Modelling of the Interaction Between Human Choriogonadotropin and Its Receptor," Protein Engineering, 7(2):205-211 (1994).
|
Griffin, et al., "Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae," Mol Cell Proteomics, 1:323-333 (2002).
|
Grundy, et al., "Regulation of the Bacillus subtilis acetate kinase gene by CcpA." J Bacteriol, 175(22):7348-7355 (1993).
|
Guelzim, et al., "Topological and causal structure of the yeast transcriptional regulatory network," Nat Genet, 31(1):60-63 (2002).
|
Guetsova, et al., "The isolation and characterization of Saccharomyces cerevisiae mutants that constitutively express purine biosynthetic genes," Genetics, 147(2):383-397 (1997).
|
Hardison, et al., "Globin Gene Server: A Prototype E-Mail Database Server Featuring Extensive Multiple Alignments and Data Compilation for Electronic Genetic Analysis," Genomics, 21(2):344-353 (1994).
|
Hartig et al., "Differentially regulated malate synthase genes participate in carbon and nitrogen metabolism of S. cerevisiae.," Nucleic Acids Res, 20(21):5677-5686 (1992).
|
Hasty, et al., "Computational Studies of Gene Regulatory Networks: In Numero Molecular Biology," Nat Rev Genet, 2(4):268-279 (2001).
|
Hata, et al., "Characterization of a Saccharomyces cerevisiaemutant, N22, defective in ergosterol synthesis and preparation of [28-14C]ergosta-5,7-dien-3 beta-ol with the mutant," J Biochem, 94(2):501-510 (1983).
|
Hatzimanikatis, et al., "Analysis and Design of Metabolic Reaction Networks Via Mixed-Interger linear Optimization," AIChE Journal, 42(5):1277-1292 (1996).
|
Hazell, et al., "How Helicobacter pylori works: an overview of the metabolism of Helicobacter pylori," Helicobacter, 2(1):1-12 (1997).
|
Heijnen, et al., "Application of balancing methods in modeling the penicillin fermentation," Biotechnology & Bioeng., 21:2175-2201 (1979).
|
Heinisch, et al., "Investigation of two yeast genes encoding putative isoenzymes of phosphoglycerate mutase.," Yeast, 14(3):203-213 (1998).
|
Heinrich, et al., "Metabolic regulation and mathematical models," Prog Biophys Mol Biol, 32(1):1-82 (1977).
|
Heinrich, et al., "Stoichiometric Analysis," The Regulation of Cellular Systems, xix:75-111 and 372, Chapman & Hall, New York (1996).
|
Henriksen, et al., "Growth energetics and metabolism fluxes in continuous cultures of Penicillium chrysogenum," J of Biotechnol, 45(2):149-164 (1996).
|
Heyer, et al., "Exploring expression data: identification and analysis of coexpressed genes," Genome Res, 9(11):1106-1115 (1999).
|
Holter, et al., "Dynamic modeling of gene expression data," Proc Natl Acad Sci U.S.A., 98(4):1693-1698 (2001).
|
Holter, et al., "Fundamental patterns underlying gene expression profiles: simplicity from complexity," Proc Natl Acad Sci U.S.A., 97:8409-9414 (2000).
|
Home page from URL: web.archive.org/web/20021126044821/http://tula.cifn.unam.mx:8850/regulondb/regulon-intro.frameset; obtained on Sep. 18, 2009.
*
|
Home page from URL: web.archive.org/web/20041125063300/http://wit.acs.ani.org; What is There (WIT), Obtained Nov. 23, 2008.
*
|
Home page from URL: web.archive.org/web/20050201083239/igweb.integratedgenomics.com/MPW/, Metabolic pathways database (MPW), obtained on Sep. 18, 2009.
*
|
Home page from URL: web.archive.org/web/20070228190312/http://systemsbiology.ucsd.edu, obtained on Sep. 18, 2009.
*
|
Houghten, "Generation and use of synthetic peptide combinatorial libraries for basic research and drug discovery," Nature, 354(6348):84-86 (1991).
|
Hughes, et al., "Functional discovery via a compendium of expression profiles," Cell, 102(1):109-126 (2000).
|
Hughes, et al., "Helicobacter pylori porCDAB and oorDABC genes encode distinct pyruvate: flavodoxin and 2-oxoglutarate:acceptor oxidoreductases which mediate electron transport to NADP," J Bacteriol, 180(5):1119-1128 (1998).
|
Ideker, et al., "Integrated Genomic and Proteomic Analyses of a Systematically Perturbed Metabolic Network," Science, 292(5518):929-934 (2001).
|
Ince, JE and Knowles, CJ, "Ethylene formation by cell-free extracts of Escherichia coli," Arch Microbiol, 146(2):151-158 (1986).
|
Ishii, et al., "DBTBS: a database of Bacillus subtilis promoters and transcription factors," Nucleic Acids Res, 29(1):278-280 (2001).
|
Iyer, et al., "Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF," Nature, 409(6819):533-538 (2001).
|
Jamshidi, et al., "Dynamic simulation of the human red blood cell metabolic network," Bioinformatics, 17(3):286-287 (2001).
|
Jamshidi, et al., "In silico model-driven assessment of the effects of single nucleoptide polymorphins (SNPs) on human red blood cell-metabolism," Genome Research, 12(11):1687-1692 (2002).
|
Jenkins, LS and Nunn, WD, "Genetic and molecular characterization of the genes involved in short-chain fatty acid degradation in Escherichia coli: the ato system," J Bacteriol, 169(1):42-52 (1987).
|
Jenssen, et al., "A Literature Network of Human Genes for High-Throughput Analysis of Gene Expression," Nat Genet, 28(1):21-28 (2001).
|
Jorgensen, et al., "Metabolic flux distributions in Penicillium chrysogenum during fed-batch cultivations." Biotechnol Bioeng, 46(2):117-131 (1995).
|
Joshi, A and Palsson, BO, "Metabolic dynamics in the human red cell. Part I—A comprehensive kinetic model," J Theor Biol, 141(4):515-528 (1989).
|
Juty, et al., "Simultaneous Modeling of Metabolic, Genetic, and Product-Interaction Networks," Briefings in Bioinformatics, 2(3):223-232 (2001).
|
Kanehisa, M and Goto, S, "Kyoto Encyclopedia of Genes and Genomes database (KEGG)," Nucleic Acids Res, 28(1):27-30 (2000).
|
Karp, "An ontology for biological function based on molecular interactions," Bioinformatics, 16(3):269-285 (2000).
|
Karp, et al., "Eco Cyc: encyclopedia of Escherichia coli genes and metabolism," Nucleic Acids Res, 27(1):55-58 (1999).
|
Karp, et al., "HinCyc: A knowledge base of the complete genome and metabolic pathways of H. influenzae," Proc Int Conf Intell Syst Mol Biol, 4:116-124 (1996).
|
Karp, et al., "Integrated pathway-genome databases and their role in drug discovery.," Trends Biotechnol, 17(7):275-281 (1999).
|
Karp, et al., "The EcoCyc and MetaCyc databases," Nucleic Acids Resarch, 28(1):56-59 (2000).
|
Kather, et al., "Another unusual type of citric acid cycle enzyme in Helicobacter pylori: the malate:quinone oxidoreductase," J Bacteriol, 182(11):3204-3209 (2000).
|
Keating, et al., "An ethanologenic yeast exhibiting unusual metabolism in the fermentation of lignocellulosic hexose sugars," J Ind Microbiol Biotechnol, 31(5):235-244 (2004).
|
Kelly, "The physiology and metabolism of the human gastric pathogen Helicobacter pylori," Adv. Microb. Physiol. 40:137-189 (1998).
|
Kim, et al., "Saccharomyces cerevisiae contains two functional citrate synthase genes.," Mol Cell Biol, 6(6):1936-1942 (1986).
|
Kirkman, et al., "Red cell NADP+ and NADPH in glucose-6-phosphate dehydrogenase deficiency," Journal of Clinical Investigation, 55(4):875-878 (1975).
|
Kremling, et al., "The organization of metabolic reaction networks. III. Application for diauxic growth on glucose and lactose," Metab. Eng. 3(4):362-379 (2001).
|
Kunst et al. The project of sequencing the entire Bacillus substilis genome. Research in Microbiology. 1991, vol. 142, pp. 905-912.
*
|
Kunst, et al., "The Complete Genome Sequence of the Gram-positive Bacterium Bacillus subtilus," Nature, 390(6557):249-256 (1997).
|
Lacroute, "Regulation of pyrimidine biosynthesis in Saccharomyces cerevisiae" J Bacteriol, 95(3):824-832 (1968).
|
Latif, F and Rajoka, MI, "Production of ethanol and xylitol from corn cobs by yeasts," Bioresour Technol, 77(1):57-63 (2001).
|
Lendenmann, U and Egli, T, "Is Escherichia coli growing in glucose-limited chemostat culture able to utilize other sugars without lag?," Microbiology, 141(Pt 1):71-78 (1995).
|
Leyva-Vasquez, MA and Setlow, P, "Cloning and nucleotide sequences of the genes encoding triose phosphate isomerase, phosphoglycerate mutase, and enolase from Bacillus subtilis," J Bacteriol, 176(13):3903-3910 (1994).
|
Li, C and Wong, WH, "Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection," Proc Natl Acad Sci U.S.A., 98(1):31-36 (2001).
|
Liao, et al., "Pathway Analysis, Engineering, and Physiological Considerations for Redirecting Central Metabolism," Biotechnol Bioeng, 52(1):129-140 (1996).
|
Liao, JC and Oh, MK, "Toward predicting metabolic fluxes in metabolically engineered strains," Metab Eng,1(3):214-223 (1999).
|
Link, et al., "Methods for generating precise deletions and insertions in the genome of wild-type Escherichia coli: Application to open reading frame characterization," J Bacteriol, 179(20):6228-6237 (1997).
|
Loftus, et al., "Isolation, characterization, and disruption of the yeast gene encoding cytosolic NADP-specific isocitrate dehydrogenase," Biochemistry, 33(32):9661-9667 (1994).
|
Lopez, et al., "The yeast inositol monophosphatase is a lithium- and sodium-sensitive enzyme encoded by a non-essential gene pair," Mol Microbiol, 31(4):1255-1264 (1999).
|
Mahadevan and Schilling, "The effects of alternate optimal solutions in constraint-based genome-scale metabolic models," Metab. Eng. 5(4):264-276 (2003).
|
Majewski, R A. Simple Constrained Optimization View of Acetate Overflow in E. coli. Biotechnology and Bioengineering, vol. 35, pp. 732-738 (1990).
|
Marcelli, et al., "The respiratory chain of Helicobacter pylori: identification of cytochromes and the effects of oxygen on cytochrome and menaquinone levels," FEMS Microbiol Lett, 138(1):59-64 (1996).
|
Marshall and Warren, "Unidentified curved bacilli in the stomach of patients with gastritis and peptic ulceration," Lancet 1(8390):1311-1315 (1984).
|
McAdams and Shapiro, "Circuit simulation of genetic networks." Science 269(5224):650-656 (1995).
|
McAdams, HH and Arkin, A, "Simulation of Prokaryotic Genetic Circuits," Annual Review of Biophysics and Biomolecular Structure, 27:199-224 (1998).
|
McAlister-Henn, L and Thompson, LM, "Isolation and expression of the gene encoding yeast mitochondrial malate dehydrogenase.," J Bacteriol, 169(11):5157-5166 (1987).
|
McGee, D.J., "Helicobacter pylori rocF is required for arginase activity and acid protection in vitro but is not essential for colonization of mice or for urease activity," J Bacteriol, 165(1):65-76 (1998).
|
Meldrum, "Automation for genomics, part one: preparation for sequencing," Genome Res, 10(8):1081-1092 (2000).
|
Mendes, P and Kell, D, "Non-linear optimization of biochemical pathways: Applications to metabolic engineering and parameter estimation," Bioinformatics, 14(10):869-883 (1998).
|
Mendz and Hazell, "Fumarate catabolism in Helicobacter pylori," Biochem. Mol. Biol. Int. 31(2):325-332 (1993).
|
Mendz et al., "Fumarate reductase: a target for therapeutic intervention against Helicobacter pylori," Arch. Biochem. Biophys. 321(1):153-159 (1995).
|
Mendz et al., "Glucose utilization and lactate production by Helicobacter pylori," J. Gen. Microbiol. 139(12):3023-3028 (1993).
|
Mendz et al., "Salvage synthesis of purine nucleotides by Helicobacter pylori," J. Appl. Bacteriol. 77(6):674-681 (1994).
|
Mendz, et al., "Characterisation of glucose transport in Helicobacter pylori," Biochim Biophys Acta, 1244(2-3):269-276 (1995).
|
Mendz, et al., "Characterization of fumarate transport in Helicobacter pylori," J Membr Biol, 165(1):65-76 (1998).
|
Mendz, et al., "De novo synthesis of pyrimidine nucleotides by Helicobacter pylon," J Appl Bacteriol, 77(1):1-8 (1994).
|
Mendz, et al., "In situ characterization of Helicobacter pylori arginase," Biochim Biophys Acta, 1388(2):465-477 (1998).
|
Mendz, et al., "Purine metabolism and the microaerophily of Helicobacter pylori," Arch Microbiol, 168(6):448-456 (1997).
|
Mendz, et al., "The Entner-Doudoroff pathway in Helicobacter pylori," Arch Biochem Biophys, 312(2):349-356 (1994).
|
Mendz, GL and Hazell SL, "Aminoacid utilization by Helicobacter pylori," Int J Biochem Cell Biol, 27(10):1085-1093 (1995).
|
Mendz, GL and Hazell, SL, "Glucose phosphorylation in Helicobacter pylori," Arch Biochem Biophys, 300(1):522-525 (1993).
|
Mendz, GL, et al., "Pyruvate metabolism in Helicobacter pylori," Arch Microbiol, 162(3):187-192 (1994).
|
Mewes, et al., "MIPS: A database for genomes and protein sequences," Nucleic Acids Research, 30(1):31-34 (2002).
|
Mitchell, "The GLN1 locus of Saccharomyces cerevisiae encodes glutamine synthetase," Genetics, 111(2):243-258 (1985).
|
Moszer, "The Complete Genome of Bacillus subtilis: From Sequence Annotation to Data Management and Analysis," FEBS Lett, 430(1-2):28-36 (1998).
|
Moszer, et al., "SubtiList: the reference database for the Bacillus subtilis genome," Nucleic Acids Res, 30(1):62-65 (2002).
|
Mulquiney, PJ and Kuchel, PW, "Model of 2,3-bisphosphoglycerate metabolism in the human erythrocyte based on detailed enzyme kinetic equations: computer simulation and metabolic control analysis," Biochem J, 342(Pt 3):597-604 (1999).
|
Murray, M and Greenberg, ML, "Expression of yeast INM1 encoding inositol monophosphatase is regulated by inositol, carbon source and growth stage and is decreased by lithium and valproate," Mol Microbiol, 36(3):651-661 (2000).
|
Nedenskov, "Nutritional requirements for growth of Helicobacter pylori," Appl Environ Microbiol, 60(9):3450-3453 (1994).
|
Nissen, et al., "Expression of a cytoplasmic transhydrogenase in Saccharomyces cerevisiae results in formation of 2-oxoglutarate due to depletion of the NADPH pool," Yeast, 18(1):19-32 (2001).
|
Nissen, et al., "Flux distributions in anaerobic, glucose-limited continuous cultures of Saccharomyces cerevisiae," Microbiology, 143(Pt 1):203-218 (1997).
|
Ogasawara, "Systematic function analysis of Bacillus subtilis genes," Res Microbiol, 151(2):129-134 (2000).
|
Ogata, et al., "KEGG: Kyoto Encyclopedia of Genes and Genomes," Nucleic Acids Res, 27(1):29-34 (1999).
|
Oh, MK and Liao, JC, "Gene expression profiling by DNA microarrays and metabolic fluxes in Escherichia coli," Biotech Prog, 16:278-286 (2000).
|
Olsson, et al., "Separate and simultaneous enzymatic hydrolysis and fermentation of wheat hemicellulose with recombinant xylose utilizing Saccharomyces cerevisiae," Appl Biochem Biotechnol, 129-132:117-129 (2006).
|
Otto, et al., "A mathematical model for the influence of fructose 6-phosphate, ATP, potassium, ammonium and magnesium on the phosphofructokinase from rat erythrocytes," Eur J Biochem, 49(1):169-178 (1974).
|
Ouzounis, CA and Karp, PD, "Global Properties of the Metabolic Map of Escherichia coli," Genome Res, 10(4):568-576 (2000).
|
Overbeek, et al., "WIT: Integrated System for High-Throughput Genome Sequence Analysis and Metabolic Reconstruction" Nucleic Acids Res, 28(1):123-125 (2000).
|
Overkamp, et al., "In vivo analysis of the mechanisms for oxidation of cytosolic NADH by Saccharomyces cerevisiae mitochondria," J Bacteriol, 182(10):2823-2830 (2000).
|
Ozcan, S., Freidel, K., Leuker, A. & Ciriacy, M., "Glucose uptake and catabolite repression in dominant HTR1 mutants of Saccharomyces cerevisiae.," J Bacteriol, 175(17):5520-5528 (1993).
|
Pallotta, et al., "Saccharomyces cerevisiae mitochondria can synthesise FMN and FAD from externally added riboflavin and export them to the extramitochondrial phase," FEBS Lett, 428(3):245-249 (1998).
|
Palmieri, et al., "Identification and functions of new transporters in yeast mitochondria," Biochim Biophys Acta, 1459(2-3):363-369 (2000).
|
Palmieri, et al., "Identification of the yeast ACR1 gene product as a succinate-fumarate transporter essential for growth on ethanol or acetate," FEBS Lett, 417(1):114-118 (1997).
|
Palmieri, et al., "Identification of the yeast mitochondrial transporter for oxaloacetate and sulfate," J Biol Chem, 274(32):22184-22190 (1999).
|
Palmieri, et al., "Yeast mitochondrial carriers: bacterial expression, biochemical identification and metabolic significance," J Bioenerg Biomembr, 32(1):67-77 (2000).
|
Palsson, "The Challenges of in Silico (2000). Biology," Nat Biotechnol, 18(11):1147-1150 (2000).
|
Palsson, "What Lies Beyond Bioinformatics," Nat. Biotech. 15:3-4 (1997).
|
Palsson, B., What lies Beyond Bioinformatics Nature Biotechnology vol. 15:3-4 (1997).
|
Papin, et al., "The genome-scale metabolic extreme pathway structure in Haemophilus influenzae shows significant network redundancy," J Theor Biol, 215(1):67-82 (2002).
|
Parks, "Metabolism of sterols in yeast," CRC Crit Rev Microbiol, 6(4):301-341 (1978).
|
Parks, et al., "Use of sterol mutants as probes for sterol functions in the yeast, Saccharomyces cerevisiae," Crit Rev Biochem Mol Biol, 34(6):399-404 (1999).
|
Patel and West, "Degradation of the pyrimidine bases uracil and thymine by Escherichia coli B" Microbios. 49(199):107-113 (1987).
|
Paulsen, et al., "Unified inventory of established and putative transporters encoded within the complete genome of Saccharomyces cerevisiae," FEBS Lett, 430(1-2):116-125 (1998).
|
Pearson, et al., "Comparison of DNA Sequences With Protein Sequences," Genomics, 46(1):24-36 (1997).
|
Pennisi, Laboratory Workhorse Decoded, Science, 277:1432-1434, Sep. 1997.
*
|
Persson, et al., "Phosphate permeases of Saccharomyces cerevisiae: structure, function and regulation," Biochim Biophys Acta, 1422(3):255-272 (1999).
|
Peterson, et al., "The Comprehensive Microbial Resource," Nucleic Acids Res, 29(1):123-125 (2001).
|
Pharkya, et al., "Exploring the overproduction of amino acids using the bilevel optimization framework OptKnock," Biotechnol Bioeng, 84(7):887-899 (2003).
|
Phelps, et al., "Metabolomics and microarrays for improved understanding of phenotypic characteristics controlled by both genomics and environmental constraints," Curr Opin Biotechnol, 13(1):20-24 (2002).
|
Pitson, et al., "The tricarboxylic acid cycle of Helicobacter pylori," Eur J Biochem, 260(1):258-267 (1999).
|
Pramanik et al., Stoichiometric model of Escherichia coli metabolism: Incorporation of growth rate dependent biomass composition and mechanistic energy requierements, Biotechnology and Bioengineering, vol. 56, No. 4:398-421 (1997).
|
Price, et al., "Determination of redundancy and systems properties of the metabolic network of Helicobacter pylori using genome-scale extreme pathway analysis," Genome Res, 12(5):760-769 (2002).
|
Price, et al., "Genome-scale models of microbial cells: evaluating the consequences of constraints," Nat Rev Microbiol, 2(11):886-897 (2004).
|
Price, et al., "Network-based analysis of metabolic regulation in the human red blood cell," J Theor Biol, 225(2):185-194 (2003).
|
Przybyla-Zawislak, et al., "Genes of succinyl-CoA ligase from Saccharomyces cerevisiae.," Eur J Biochem, 258(2):736-743 (1998).
|
Qian, et al., "Ethanol production from dilute-Acid softwood hydrolysate by co-culture," Appl Biochem Biotechnol, 134(3):273-284 (2006).
|
Raclot et al., "Selective release of human adipocyte fatty acids according to molecular structure," Biochem. J. 324 (Pt3):911-915 (1997).
|
Reed, et al., "An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)," Genome Biol, 4(9):R54 (2003).
|
Reed, JL and Palsson, BO, "Thirteen years of building constraint-based in silico models of Escherichia coli" J Bacteriol, 185(9):2692-2699 (2003).
|
Regenberg, et al., "Substrate specificity and gene expression of the amino-acid permeases in Saccharomyces cerevisiae," Curr Genet, 36(6):317-328 (1999).
|
Remize, et al., "Engineering of the pyruvate dehydrogenase bypass in Saccharomyces cerevisiae: role of the cytosolic Mg(2+) and mitochondrial K(+) acetaldehyde dehydrogenases Ald6p and Ald4p in acetate formation during alcoholic fermentation," Appl Environ Microbiol, 66(8):3151-3159 (2000).
|
Ren, et al., "Genome-wide location and function of DNA binding proteins," Science, 290(5500):2306-2309 (2000).
|
Repetto, B and Tzagoloff, A, "In vivo assembly of yeast mitochondrial alpha-ketoglutarate dehydrogenase complex," Mol Cell Biol, 11(8):3931-3939 (1991).
|
Reynolds, DJ and Penn, CW, "Characteristics of Helicobacter pylori growth in a defined medium and determination of its amino acid requirements," Microbiology, 140(Pt. 10):2649-2656 (1994).
|
Rhee, et al., "Activation of gene expression by a ligand-induced conformational change of a protein-DNA complex," J Biol Chem, 273(18):11257-11266 (1998).
|
Romero, PR and Karp, P, "Nutrient-Related Analysis of Pathway/Genome Databases," Pac Symp Biocomput, 471-482 (2001).
|
Saier, MH, "Genome sequencing and informatics: new tools for biochemical discoveries," Plant Physiol, 117(4):1129-1133 (1998).
|
Salgado, et al., Nucleic Acids Res, 29(1):72-74 (2001).
|
Salmon, et al., "Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNR," J Biol Chem, 278(32):29837-29855 (2003).
|
Sauer et al., "Metabolic Capacity of Bacillus subtilis for the Production of Purine Nucleosides, Riboflavin, and Folic Acid," Biotechnol. Bioeng, 59(2):227-238 (1998).
|
Sauer, et al., "Metabolic flux ratio analysis of genetic and environmental modulations of Escherichia coli central carbon metabolism," J Bacteriol, 181(21):6679-6688 (1999).
|
Sauer, et al., Metabolic Capacity of Bacillus subtilis for the Production of Purine Nucleosides, Riboflavin, and Folic Acid Biotechnology and Bioengineering, vol. 59, No. 2:227-238 (1998).
|
Sauer, U and Bailey, JE, "Estimation of P-to-O Ratio in Bacillus subtilis and Its Influence on Maximum Riboflavin Yield," Biotechnol Bioeng, 64(6):750-754 (1999).
|
Sauer, Uwe, "Evolutionary Engineering of Industrially Important Microbial Phenotypes," Adv in Biochem Eng Biotechnol, 73:129-169 (2001).
|
Savageau, "Biochemical systems analysis. I. Some mathematical properties of the rate law for the component enzymatic reactions," J Theor Biol, 25(3):365-369 (1969).
|
Savinell and Palsson, "Network Analysis of Intermediary Metabolism using Linear Optimization. I. Development of Mathematical Formalism," J Theor Biol 154:421-454 (1992).
|
Savinell and Palsson, "Network Analysis of Intermediary Metabolism using Linear Optimization. II. Interpretation of Hybridoma Cell Metabolism," J. Theor. Biol. 154:455-473 (1992).
|
Schaaff-Gerstenschlager, I and Zimmermann, FK, "Pentose-phosphate pathway in Saccharomyces cerevisiae: analysis of deletion mutants for transketolase, transaldolase, and glucose 6-phosphate dehydrogenase," Curr Genet, 24(5):373-376 (1993).
|
Schaff, et al., "the Virtual cell" Proceedings of the Pacific Symposium on Biocomputing, 4:228-239 (1999).
|
Schena, et al., "Quantitative monitoring of gene expression patterns with a complementary DNA microarray," Science 270(5235):467-470 (1995).
|
Schilling and Palsson, "The Underlying Pathway Structure of Biochemical Reaction Networks," Proc. Natl. Acad. Sci. USA 95(8):4193-4198 (1998).
|
Schilling, "On Systems Biology and the Pathway Analysis of Metabolic Networks," Department of Bioengineering, University of California, San Diego: La Jolla 198-241 (2000).
|
Schilling, CH and Palsson, BO, "Assessment of the Metabolic Capabilities of Haemophilus influenzae Rd Through a Genome-scale Pathway Analysis," J Theor Biol, 203(3):249-283 (2000).
|
Schilling, CH and Palsson, BO, "The Underlying Pathway Structure of Biochemical Reaction Networks," Proc Natl Acad Sci U.S.A., 95(8):4193-4198 (1998).
|
Schilling, et al., "Combining Pathway Analysis with Flux Balance Analysis for the Comprehensive Study of Metabolic Systems," Biotechnol Bioeng, 71(4):286-306.
|
Schilling, et al., "Genome-scale metabolic model of Helicobacter pylori 26695," J Bacteriol, 184(16):4582-4593 (2002).
|
Schilling, et al., "Metabolic Pathway Analysis: Basic Concepts and Scientific Applications in the Post-genomic Era," Biotechol Prog, 15(3):296-303 (1999).
|
Schilling, et al., "Theory for the Systematic Definition of Metabolic Pathways and Their Use in Interpreting Metabolic Function from a Pathway-Oriented Perspective," J Theor Biol, 203(3):229-248 (2000).
|
Schilling, et al., Toward Metobolic Phenomics: Analysis and Genomic Data Using Flax Balances Biotechnology Progress vol. 15, No. 3:288-95 (1999).
|
Schneider, et al., "The Escherichia coli gabDTPC operon: specific gamma-aminobutyrate catabolism and nonspecific induction," J Bacteriol, 184(24):6976-6986.
|
Schuster, et al., "A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks," Nature Biotechnol, 18(3):326-332 (2000).
|
Schuster, et al., "Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering," Trends Biotechnol, 17(2):53-60 (1999).
|
Schuster, et al., "Exploring the pathway structure of metabolism: decomposition into subnetworks and application to Mycoplasma pneumoniae," Bioinformatics, 18(2):351-361 (2002).
|
Schuster, S and Hilgetag, C, "On elementary flux modes in biochemical reaction systems at steady state," J Biol Syst, 2(2):165-182 (1994).
|
Schwikowski, et al., "A network of protein-protein interactions in yeast," Nature Biotechnol, 18(12):1257-1261 (2000).
|
Scott, et al., The Pendred syndrome gene encodes a chloride-iodide transport protein. Nature Genetics, vol. 21, pp. 44-443 (1999).
|
Sedivy and Fraenkel, "Fructose bisphosphatase of Saccharomyces cerevisiae. Cloning, dusruption and regulation of the FBP1 sructural gene.," J. Mol. Biol. 186(2):307-319 (1985).
|
Selkov, et al., "A reconstruction of the metabolism of Methanococcus jannaschii from sequence data.," Gene, 197(1-2):GC11-26 (1997).
|
Selkov, et al., "Functional Analysis of Gapped Microbial Genomes: Amino Acid Metabolism of Thiobacillus Ferroxidans," Proc Natl Acad Sci U.S.A., 97(7):3509-3514 (2000).
|
Selkov, et al., "MPW: the metabolic pathways database," Nucleic Acids Res, 26(1):43-45 (1998).
|
Selkov, et al., "The metabolic pathway collection from EMP: the enzymes and metabolic pathways database," Nucleic Acids Res. 24(1):26-28 (1996).
|
Shen-Orr, et al., "Network motifs in the transcriptional regulation network of Escherichia coli," Nat Genet, 31(1):64-68 (2002).
|
Sherlock, et al., "The physiology of L-methionine catabolism to the secondary metabolite ethylene by Escherichia coli," Curr. Opin. Immunol. 12:201-205 (2000).
|
Shipston and Bunch, "The physiology of L-methionine catabolism to the secondary metabolite ethylene by Escherichia coli," J. Gen. Microbiol. 135(6), 1489-1497 (1989).
|
Silve, et al., The immunosuppressant SR 31747 blocks cell proliferation by inhibiting a steroid isomerase in Saccharomyces cerevisiae, Mol. Cell Biol. 16(6):2719-2727 (1996).
|
Six pages from URL: web.archive.org/web/2005025215224/genome-www.stanford.edu/~sherlock/cluster.html, "XCluster" software; obtained on Sep. 18, 2009.
*
|
Six pages from URL: web.archive.org/web/2005025215224/genome-www.stanford.edu/˜sherlock/cluster.html, "XCluster" software; obtained on Sep. 18, 2009.
*
|
Skouloubris, et al., "The Helicobacter pylori UreI protein is not involved in urease activity but is essential for bacterial survival in vivo," Infect Immun, 66(9):4517-4521 (1998).
|
Smith, et al., "Functional analysis of the genes of yeast chromosome V by genetic footprinting.," Science, 274(5295):2069-2074 (1996).
|
Sorlie, et al., "Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications," Proc Natl Acad Sci U.S.A., 98(19):10869-10874 (2001).
|
Stark, et al., "Amino acid utilisation and deamination of glutamine and asparagine by Helicobacter pylori," J Med Microbiol, 46(9):793-800 (1997).
|
Stephanopoulos, "Metabolic engineering," Curr Opin Biotechnol, 5(2):196-200 (1994).
|
Stryer, L., Biochemistry (2nd Edition), W.H. Freeman and Company, San Francisco, 1981, p. 288.
*
|
Summers, et al., "Saccharomyces cerevisiae cho2 mutants are deficient in phospholipid methylation and cross-pathway regulation of inositol synthesis" Genetics, 120(4):909-922 (1988).
|
Swartz, "A PURE approach to constructive biology.," Nat Biotechnol, 19(8):732-733 (2001).
|
Syvanen, "Accessing genetic variation: Genotyping single nucleotide polymorphisms.," Nat Rev Genet, 2(12):930-942 (2001).
|
Szambelan, et al., "Use of Zymomonas mobilis and Saccharomyces cerevisiae mixed with Kluyveromyces fragilis for improved ethanol production from Jerusalem artichoke tubers," Biotechnol Lett, 26(10):845-848 (2004).
|
Tamayo, et al., "Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentation," Proc Natl Acad Sci U.S.A., 96(6):2907-2912 (1999).
|
Tanaka and Zerez, "Red cell enzymopathies of the glycolytic pathway," Semin. Hematol. 27(2):165-185 (1990).
|
Tandeitnik, et al., "Modeling of biological neurons by artificial neural networks," Nineteenth Convention of Electrical and Electronics Engineers in Israel, Jerusalem, Israel, New York, NY USA, pp. 239-242 (1996).
|
Taniguchi and Tanaka, "Clarification of interactions among microorganisms and development of co-culture system for production of useful substances," Adv. Biochem. Eng. Biotechnol. 90:35-62 (2004).
|
Tao, et al., "Engineering a homo-ethanol pathway in Escherichia coli: increased glycolytic flux and levels of expression of glycolytic genes during xylose fermentation," J Bacteriol, 183(10):2979-2988 (2001).
|
ter Linde, et al., "Genome-wide transcriptional analysis of aerobic and anaerobic chemostat cultures of Saccharomyces cerevisiae," J Bacteriol, 181(24):7409-7413 (1999).
|
Thomas, "Boolean Formalization of Genetic Control Circuits," J Theor Biol, 42(3):563-585 (1973).
|
Thomas, "Logical Analyses of Systems Comprising Feedback Loops," J Theor Biol, 73(4):631-656 (1978).
|
Thomas, D and Surdin-Kerjan, Y, "Metabolism of sulfur amino acids in Saccharomyces cerevisiae," Microbiol Mol Biol Rev, 61(4):503-532 (1997).
|
Three pages from URL: web.archive.org/web/19981206132808/http://ecocyc.panbio.com/ecocyc/ecocyc.html; Ecocyc; obtained on Sep. 18, 2009.
*
|
Three pages from URL: web.archive.org/web/2007001095540/http://mips.gsf.de/proj/yeast/pathways on Jun. 6, 2008. MIPS, website: Comprehensive Yeast Genome Database-Pathways; Date Obtained Sep. 18, 2009.
*
|
Tomb, et al., "The complete genome sequence of the gastric pathogen Helicobacter pylori," Nature, 388(6642):539-547 (1997).
|
Tomita, et al., E-Cell: Software Environment for Whole-Cell Simulation: Bioinformatics, vol. 15, No. 1: 72-84 (1999).
|
Trotter, et al., "A genetic screen for aminophospholipid transport mutants identifies the phosphatidylinositol 4-kinase, STT4p, as an essential component in phosphatidylserine metabolism," J Biol Chem, 273(21):13189-13196 (1998).
|
Two pages from URL: web.archive.org/web/20060712190022/http://www.tigr.org/. The Institute for Genome Research, J. Craig Venter Institute; obtained on Sep. 18, 2009.
*
|
Two pages from URL: www.ncbi.nlm.nih.gov/sites/entrz?db=genome obtained on Jun. 15, 2009.
*
|
Uetz, et al., "A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae," Nature, 403(6770):623-627 (2000).
|
URL affymetrix.com/index.affx; Date Obtained: Sep. 18, 2009, Home page 1 page.
|
URL affymetrix.com/products/arrays/specific/ecoli antisense.affx.: Date Obtained: Sep. 18, 2009, Home page, 1 page.
|
URL asap.ahabs.wisc.edu/annotation/php/logon.php, The ASAP website.; Date Obtained: Sep. 7, 2009, Home page, 1 page.
|
URL ca.expasy.org/sprot/, protein database SWISS—PROT: Date Obtained: Jun. 15, 2009, Home page, 2 pages.
|
URL dchip.org, dChip software; Date Obtained Jun. 15, 2009.
|
URL Dictionary.com pp. 1-2 (2004), Matrix.
|
URL Dictionary.com pp. 1-2 (2004), Matrix; Date Obtained Nov. 1, 2004.
|
URL enzobio.com/lifesci—index.htm, Enzo BioArray Terminal Labeling Kit protocol; Date Obtained Sep. 18, 2009.
|
URL genetics.wisc.edu/, E. coli Genome Project at the University of Wisconsin; Date Obtained Sep. 18, 2009, Home page, 1 page total.
|
URL Genome.jp Website, KEGG Bacillus subtillis, 1-7 (2005).
|
URL Genome.jp Website, KEGG Bacillus subtillis, 1-7; Date Obtained Jun. 1, 2005, Home page.
|
URL genome.tugraz.at/Software/Genesis/Description.html, "Genesis" software; Date Obtained: Sep. 18, 2009, Home page, 1 page total.
|
URL integratedgenomics.com, ERGO from Integrated Genomics; Date Obtained Sep. 18, 2009.
|
URL ncbi.nlm.nih.gov/entrez/query.fcgi?db=Genome, The NCBI Entrez Genome database; Date Obtained Jun. 15, 2009, Home page, 1 page.
|
URL ncbi.nlm.nih.gov/LocusLink/, LocusLink database maintained by the NCBI; Date Obtained Jun. 15, 2009, Home page, 1 page.
|
URL ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/; Date Obtained Sep. 18, 2009, 1 page.
|
URL nslij-genetics.org/search—omim.html, Online Mendelian Inheritance in Man database, Center for Medical Genetics, Johns Hopkins University (Baltimore, MD) and National Center for Biotechnology Information, National Library of Medicine (Bethesda, MD); Date Obtained Sep. 18, 2009, Home page, 2 pages.
|
URL qiagen.com, Qiagen RNeasy Mini Kit; Date Obtained Sep. 18, 2009, Home page, 1 page.
|
URL rana.lbl.gov/EisenSoftware.htm, "Cluster" software; Date Obtained Sep. 18, 2009, 3 pages.
|
URL. www.i-sis.org.uk/WITBRL.php; Hoppert, M; Date Obtained Nov. 23, 2008.
|
Van den Berg, MA and Steensma, HY, "ACS2, a Saccharomyces cerevisiae gene encoding acetyl-coenzyme A synthetase, essential for growth on glucose," Eur J. Biochem, 231(3):704-713 (1995).
|
van Dijken, et al., "Alcoholic fermentation by ‘non-fermentative’ yeasts," Yeast, 2(2):123-127 (1986).
|
van Dijken, et al., "Kinetics of growth and sugar consumption in yeasts," Antonie Van Leeuwenhoek, 63(3-4):343-352 (1993).
|
Vanrolleghem, et al., "Validation of a Metabolic Network for Saccharomyces cerevisiae Using Mixed Substrate Studies," Biotechnol Prog, 12(4):434-448 (1996).
|
Varma, A and Palsson, BO, "Metabolic capabilities of Escherichia coli. II: Optimal Growth Patterns.," J Theor Biol, 165:503-522 (1993).
|
Varma, A and Palsson, BO, "Metabolic capabilities of Escherichia coli: I. Synthesis of Biosynthetic Precursors and Cofactors," J Theor Biol, 165:477-502 (1993).
|
Varma, A and Palsson, BO, "Parametric senstitivity of stoichiometric flux balance models applied to wild-type Escherichia coli metabolism," Biotechnol Bioeng, 45(1):69-79 (1995).
|
Varma, A and Palsson, BO, "Predictions for Oxygen Supply Control to Enhance Population Stability of Engineered Production Strains," Biotechnol Bioeng, 43(4):275-285 (1994).
|
Varma, A and Palsson, BO, "Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110," Appl Environ Microbiol, 60(10):3724-3731 (1994).
|
Varma, Amit, Metabolic Flux Balancing: Basic Concepts, Scientific and Practical Use. Bio Technology vol. 12, pp. 994-998, Oct. 1994.
|
Varma, et al., "Biochemical Production Capabilities of Escherichia coli," Biotechnol Bioeng, 42(1):59-73 (1993).
|
Varma, et al., "Stoichiometric Interpretation of Escherichia coli Glucose Catabolism Under Various Oxygenation Rates.," Appl Environ Microbiol, 59(8):2465-2473 (1993).
|
Varner, J and Ramkrishna, D, "Mathematical Models of Metabolic Pathways," Curr Opin Biotechnol, 10(2):146-150 (1999).
|
Velculescu, et al., "Analysing uncharted transcriptomes with SAGE," Trends Genet, 16(10):423-425 (2000).
|
Venter, et al., "Shotgun sequencing of the human genome," Science 280(5639):1540-1542 (1998).
|
Verduyn, "Physiology of yeasts in relation to biomass yields," Antonie Van Leeuwenhoek, 60(3-4):325-353 (1991).
|
Verduyn, et al., "A theoretical evaluation of growth yields of yeasts," Antonie Van Leeuwenhoek, 59(1):49-63 (1991).
|
Verduyn, et al., "Energetics of Saccharomyces cerevisiae in anaerobic glucose-limited chemostat cultures," J Gen Microbiol, 136:405-412 (1990).
|
Vissing, et al., "Paradoxically Enhanced Glucose Production During Exercise in Humans with Blocked Glycolysis Caused by Muscle Phosphofructokinase Deficiency," Neurology, 47(3):766-771 (1996).
|
Vo, et al., "Reconstruction and functional characterization of the human mitochondrial metabolic network abased on proteomic and biochemical data," J. Biol. Chem. 279(38):39532-39540 (2004).
|
Wang, et al., "Computer Control of Bakers' Yeast Production," Biotechnol and Bioeng, 21:975-995 (1979).
|
Wang, et al., "Computer-aided baker's yeast fermentations," Biotechnol and Bioeng, 19(1):69-86 (1977).
|
Waterston and Sulston, "The Human Genome Project: reaching the finish line," Science 282(5386):53-54 (1998).
|
Wen, et al., "Large-scale temporal gene expression mapping of central nervous system development," Proc Natl Acad Sci U.S.A., 95(1):334-339 (1998).
|
Wiback, SJ and Palsson, BO, "Extreme pathway analysis of human red blood cell metabolism," Biophys J, 83:808-818 (2002).
|
Wieczorke, et al., "Concurrent knock-out of at least 20 transporter genes is required to block uptake of hexoses in Saccharomyces cerevisiae," FEBS Lett, 464(3):123-128 (1999).
|
Wills and Melham, "Pyruvate carboxylase deficiency in yeast: a mutant affecting the interaction between the glyoxylate and Krebs cycles.," Arch. Biochem. Biophys. 236(2):782-791 (1985).
|
Wingender, et al., "The TRANSFAC system on gene expression regulation," Nucleic Acids Res, 29(1):281-283 (2001).
|
Winzeler, et al., "Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis," Science 285(5429):901-906 (1999).
|
Wong, P., et al., "Mathematical Model of the Lac Operon: Inducer Exclusion, Catabolite Repression, and Diauxic Growth on Glucose and Lactose," Biotechnol Prog, 13(2):132-143 (1997).
|
Xie and Wang, "Energy Metabolism and ATP Balance in Animal Cell Cultivation Using a Stoichiometrically Based Reaction Network," Biotech. Bioeng. 52:591-601 (1996).
|
Xie and Wang, "Material Balance Studies on Animal Cell Metabolism Using a Stoichiometrically Based Reaction Network," Biotech. Bioeng. 52:579-590 (1996).
|
Xie, et al., Integrated Approaches to the Design of Media and Feeding Strategies For Fed-Batch Cultures of Animal Cells: Trends in Biotechnology, GB, Elsevier Publications Cambridge: vol. 15, No. 3:109-113 (1997).
|
Yamada, et al., "Effects of common polymorphisms on the properties of recombinant human methylenetetrahydrofolate reductase," Proc Natl Acad Sci U.S.A., 98(26):14853-14858 (2001).
|
Yeung, et al., "Reverse engineering gene networks using singular value decomposition and robust regression," Proc Natl Acad Sci U.S.A., 99(9):6163-6168 (2002).
|
Yeung, et al., Bioinformatics, "Model-based clustering and data transformations for gene expression data," 17(10):977-87 (2001).
|
Yoshida, et al., "Combined transcriptome and proteome analysis as a powerful approach to study genes under glucose repression in Bacillus subtilis," Nucleic Acids Res, 29(3):683-692 (2001).
|
Zanella, A and Bianchi, P, "Red cell pyruvate kinase deficiency: from genetics to clinical manifestations," Bailliere's Best Pract Res Clin Haematol 13(1):57-81 (2000).
|
Zeng, et al., "Use of respiratory quotient as a control parameter for optimum oxygen supply and scale-up of 2,3-butanediol production under microaerobic conditions," Biotechnol. Bioeng. 44(9):1107-1114 (1994).
|
Zhu, J and Zhang, MO, "SCPD: a promoter database of the yeast Saccharomyces cerevisiae," Bioinformatics, 15(7-8):607-611 (1999).
|
Zigova, "Effect of RQ and pre-seed conditions on biomass and galactosyl transferase production during fed-batch culture of S. cerevisiae BT150," J. Biotechnol. 80(1):55-62 (2000).
|
Zweytick, et al., "Biochemical characterization and subcellular localization of the sterol C-24(28) reductase erg4p, from the yeast Saccharomyces cerevisiae," FEBS Lett, 470(1):83-87 (2000).
|